Exhibit 10.17


 


AFFYMETRIX, INC.


 


AMENDED AND RESTATED


 


2000 EQUITY INCENTIVE PLAN


 


(AS ADOPTED
EFFECTIVE MARCH 9, 2000

AND AMENDED THROUGH JUNE 23, 2008)


 

















 


TABLE
OF CONTENTS


 


	
   

  	
  Page

  
	
   

  	
   

  
	
  ARTICLE 1.
  INTRODUCTION

  	
  1

  
	
   

  	
   

  
	
  ARTICLE 2.
  ADMINISTRATION

  	
  1

  
	
   

  	
   

  
	
  2.1.

  	
  Committee Composition

  	
  1

  
	
  2.2.

  	
  Committee Responsibilities

  	
  1

  
	
  2.3.

  	
  Committee for Non-Officer Grants

  	
  1

  
	
   

  	
   

  	
   

  
	
  ARTICLE 3. SHARES
  AVAILABLE FOR GRANTS

  	
  2

  
	
   

  	
   

  
	
  3.1.

  	
  Basic Limitation

  	
  2

  
	
  3.2.

  	
  Additional Shares

  	
  2

  
	
  3.3.

  	
  Dividend Equivalents

  	
  2

  
	
   

  	
   

  	
   

  
	
  ARTICLE 4.
  ELIGIBILITY

  	
  2

  
	
   

  	
   

  
	
  4.1.

  	
  Incentive Stock Options

  	
  2

  
	
  4.2.

  	
  Other Grants

  	
  2

  
	
   

  	
   

  	
   

  
	
  ARTICLE 5. OPTIONS

  	
  3

  
	
   

  	
   

  
	
  5.1.

  	
  Stock Option Agreement

  	
  3

  
	
  5.2.

  	
  Number of Shares

  	
  3

  
	
  5.3.

  	
  Exercise Price

  	
  3

  
	
  5.4.

  	
  Exercisability and Term

  	
  3

  
	
  5.5.

  	
  Effect of Change in Control

  	
  3

  
	
  5.6.

  	
  Modification or Assumption of Options

  	
  3

  
	
  5.7.

  	
  Buyout Provisions

  	
  4

  
	
   

  	
   

  	
   

  
	
  ARTICLE 6. PAYMENT
  FOR OPTION SHARES

  	
  4

  
	
   

  	
   

  
	
  6.1.

  	
  General Rule

  	
  4

  
	
  6.2.

  	
  Surrender of Stock

  	
  4

  
	
  6.3.

  	
  Exercise/Sale

  	
  4

  
	
  6.4.

  	
  Other Forms of Payment

  	
  4

  
	
   

  	
   

  	
   

  
	
  ARTICLE 7. STOCK
  APPRECIATION RIGHTS

  	
  4

  
	
   

  	
   

  
	
  7.1.

  	
  SAR Agreement

  	
  4

  
	
  7.2.

  	
  Number of Shares

  	
  5

  
	
  7.3.

  	
  Exercise Price

  	
  5

  
	
  7.4.

  	
  Exercisability and Term

  	
  5

  
	
  7.5.

  	
  Effect of Change in Control

  	
  5

  
	
  7.6.

  	
  Exercise of SARs

  	
  5

  
	
  7.7.

  	
  Modification or Assumption of SARs

  	
  5

  



 


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  ARTICLE 8.
  RESTRICTED SHARES

  	
  6

  
	
   

  	
   

  
	
  8.1.

  	
  Restricted Stock Agreement

  	
  6

  
	
  8.2.

  	
  Payment for Awards

  	
  6

  
	
  8.3.

  	
  Vesting Conditions

  	
  6

  
	
  8.4.

  	
  Voting and Dividend Rights

  	
  6

  
	
   

  	
   

  	
   

  
	
  ARTICLE 9. STOCK
  UNITS AND RESTRICTED STOCK UNITS

  	
  6

  
	
   

  	
   

  
	
  9.1.

  	
  Stock Unit Agreement

  	
  6

  
	
  9.2.

  	
  Payment for Awards

  	
  6

  
	
  9.3.

  	
  Vesting Conditions

  	
  7

  
	
  9.4.

  	
  Voting and Dividend Rights

  	
  7

  
	
  9.5.

  	
  Form and Time of Settlement of Stock Units

  	
  7

  
	
  9.6.

  	
  Death of Recipient

  	
  7

  
	
  9.7.

  	
  Creditors’ Rights

  	
  7

  
	
   

  	
   

  	
   

  
	
  ARTICLE 10. OTHER
  EQUITY-BASED AWARDS

  	
  8

  
	
   

  	
   

  
	
  ARTICLE 11.
  PERFORMANCE-BASED AWARDS

  	
  8

  
	
   

  	
   

  
	
  11.1.

  	
  Performance Awards Generally

  	
  8

  
	
  11.2.

  	
  Performance Awards Granted to Covered Employees

  	
  8

  
	
  11.3.

  	
  Written Determinations

  	
  10

  
	
   

  	
   

  	
   

  
	
  ARTICLE 12.
  PROTECTION AGAINST DILUTION

  	
  10

  
	
   

  	
   

  
	
  12.1.

  	
  Adjustments

  	
  10

  
	
  12.2.

  	
  Dissolution or Liquidation

  	
  11

  
	
  12.3.

  	
  Reorganizations

  	
  11

  
	
   

  	
   

  	
   

  
	
  ARTICLE 13.
  DEFERRAL OF AWARDS

  	
  11

  
	
   

  	
   

  
	
  ARTICLE 14. AWARDS
  UNDER OTHER PLANS

  	
  12

  
	
   

  	
   

  
	
  ARTICLE 15. PAYMENT
  OF DIRECTOR’S FEES IN SECURITIES

  	
  12

  
	
   

  	
   

  
	
  15.1.

  	
  Effective Date

  	
  12

  
	
  15.2.

  	
  Elections to Receive NSOs, Restricted Shares or Stock Units

  	
  12

  
	
  15.3.

  	
  Number and Terms of NSOs, Restricted Shares or Stock Units

  	
  12

  
	
   

  	
   

  	
   

  
	
  ARTICLE 16.
  LIMITATION ON RIGHTS

  	
  12

  
	
   

  	
   

  
	
  16.1.

  	
  Retention Rights

  	
  12

  
	
  16.2.

  	
  Stockholders’ Rights

  	
  12

  
	
  16.3.

  	
  Regulatory Requirements

  	
  13

  
	
   

  	
   

  	
   

  
	
  ARTICLE 17.
  WITHHOLDING TAXES

  	
  13

  
	
   

  	
   

  
	
  17.1.

  	
  General

  	
  13

  
	
  17.2.

  	
  Withholding in Shares

  	
  13

  



 


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  ARTICLE 18. FUTURE
  OF THE PLAN

  	
  13

  
	
   

  	
   

  
	
  18.1.

  	
  Term of the Plan

  	
  13

  
	
  18.2.

  	
  Amendment or Termination

  	
  13

  
	
  18.3

  	
  No Repricings

  	
  13

  
	
   

  	
   

  	
   

  
	
  ARTICLE 19.
  DEFINITIONS

  	
  14

  
	
   

  	
   

  
	
  ARTICLE 20.
  EXECUTION

  	
  17

  



 


iii

















 


AFFYMETRIX, INC.


 


AMENDED AND RESTATED

2000 EQUITY INCENTIVE PLAN


 


ARTICLE
1.    INTRODUCTION.


 


The Plan was adopted by the Board effective March 9,
2000 and amended and restated through June 23, 2008. The purpose of the
Plan is to promote the long-term success of the Company and the creation of
stockholder value by (a) encouraging Employees, Outside Directors and
Consultants to focus on critical long-range objectives, (b) encouraging
the attraction and retention of Employees, Outside Directors and Consultants
with exceptional qualifications and (c) linking Employees, Outside
Directors and Consultants directly to stockholder interests through increased
stock ownership. The Plan seeks to achieve this purpose by providing for Awards
in the form of Restricted Shares, Stock Units, Options (which may constitute
incentive stock options or nonstatutory stock options) or stock appreciation
rights.


 


The Plan shall be governed by, and construed
in accordance with, the laws of the State of Delaware (except for choice-of-law
provisions).


 


ARTICLE
2.    ADMINISTRATION.


 


2.1.         Committee
Composition. 
The Plan shall be administered by the Committee. The Committee shall
consist exclusively of two or more directors of the Company, who shall be
appointed by the Board. In addition, except as otherwise determined by the
Board, the composition of the Committee shall satisfy:


 


(a)           Such requirements as
the Securities and Exchange Commission may establish for administrators acting
under plans intended to qualify for exemption under Rule 16b-3 (or its
successor) under the Exchange Act; and


 


(b)           Such requirements as
the Internal Revenue Service may establish for outside directors acting under
plans intended to qualify for exemption under section 162(m)(4)(C) of
the Code.


 


2.2.         Committee
Responsibilities. 
The Committee shall (a) select the Employees, Outside Directors and
Consultants who are to receive Awards under the Plan, (b) determine the
type, number, vesting requirements and other features and conditions of such
Awards, (c) interpret the Plan and (d) make all other decisions
relating to the operation of the Plan. The Committee may adopt such rules or
guidelines as it deems appropriate to implement the Plan. The Committee’s
determinations under the Plan shall be final and binding on all persons.


 


2.3.         Committee
for Non-Officer Grants.  The Board may also appoint another committee
of the Board, which shall be composed of one or more directors of the Company
who need not satisfy the requirements of Section 2.1. Such other committee
may administer the Plan 


 

















 


with respect to Employees and Consultants who are not considered
officers or directors of the Company under Section 16 of the Exchange Act,
may grant Awards under the Plan to such Employees and Consultants and may
determine all features and conditions of such Awards. Within the limitations of
this Section 2.3, any reference in the Plan to the Committee shall include
such secondary committee.


 


ARTICLE 3.    SHARES
AVAILABLE FOR GRANTS.


 


3.1.         Basic
Limitation. Common Shares issued pursuant to the Plan
may be authorized but unissued shares or treasury shares. The aggregate number
of Options, SARs, Stock Units and Restricted Shares awarded under the Plan
shall not exceed (a) 11,700,000 (from initial adoption of the Plan in
2000, after an increase of 4,200,000 shares on June 11, 2008) plus (b) the
additional Common Shares described in Section 3.2. The limitations of this
Section 3.1 and Section 3.2 shall be subject to adjustment pursuant
to Article 12.


 


3.2.         Additional
Shares. If Restricted Shares are forfeited, then such
Common Shares shall again become available for Awards under the Plan. If Stock
Units, Options or SARs are forfeited or terminated for any reason before being
exercised, or if Common Shares are tendered or withheld in satisfaction or
partial satisfaction of any tax withholding obligations, then the corresponding
Common Shares shall again become available for Awards under the Plan. If Stock
Units are settled, then only the number of Common Shares (if any) actually
issued in settlement of such Stock Units shall reduce the number available
under Section 3.1 and the balance shall again become available for Awards
under the Plan. If SARs are exercised, then only the number of Common Shares
(if any) actually issued in settlement of such SARs shall reduce the number
available under Section 3.1 and the balance shall again become available
for Awards under the Plan. The foregoing notwithstanding, the aggregate number
of Common Shares that may be issued under the Plan upon the exercise of ISOs
shall not be increased when Restricted Shares are forfeited or Common Shares
are not issued pursuant to Stock Units, Options or SARs.


 


3.3.         Dividend
Equivalents. Any dividend equivalents paid or credited
under the Plan shall not be applied against the number of Restricted Shares,
Stock Units, Options or SARs available for Awards, whether or not such dividend
equivalents are converted into Stock Units.


 


ARTICLE 4.    ELIGIBILITY.


 


4.1.         Incentive
Stock Options. Only Employees who are common-law
employees of the Company, a Parent or a Subsidiary shall be eligible for the
grant of ISOs. In addition, an Employee who owns more than 10% of the total
combined voting power of all classes of outstanding stock of the Company or any
of its Parents or Subsidiaries shall not be eligible for the grant of an ISO
unless the requirements set forth in Section 422(c)(6) of the Code
are satisfied.


 


4.2.         Other
Grants. Employees, Outside Directors and Consultants
shall be eligible for the grant of Restricted Shares, Stock Units, NSOs or
SARs.


 


2

















 


ARTICLE 5.    OPTIONS.


 


5.1.         Stock
Option Agreement. Each grant of an Option under the
Plan shall be evidenced by a Stock Option Agreement between the Optionee and
the Company. Such Option shall be subject to all applicable terms of the Plan
and may be subject to any other terms that are not inconsistent with the Plan.
The Stock Option Agreement shall specify whether the Option is an ISO or an
NSO. The provisions of the various Stock Option Agreements entered into under
the Plan need not be identical. Options may be granted in consideration of a
reduction in the Optionee’s other compensation.


 


5.2.         Number
of Shares. Each Stock Option Agreement shall specify
the number of Common Shares subject to the Option and shall provide for the
adjustment of such number in accordance with Article 12. Options granted
to any Optionee in a single fiscal year of the Company shall not cover more
than 1,000,000 Common Shares. The limitations set forth in the preceding
sentence shall be subject to adjustment in accordance with Article 12.


 


5.3.         Exercise
Price. Each Stock Option Agreement shall specify the
Exercise Price; provided that the Exercise Price shall in no event be less than
100% of the Fair Market Value of a Common Share on the date of grant. In the
case of an NSO, a Stock Option Agreement may specify an Exercise Price that
varies in accordance with a predetermined formula while the NSO is outstanding.


 


5.4.         Exercisability
and Term. Each Stock Option Agreement shall specify
the date or event when all or any installment of the Option is to become
exercisable. The Stock Option Agreement shall also specify the term of the
Option; provided that the term of an Option shall in no event exceed
10 years from the date of grant. A Stock Option Agreement may provide for
accelerated exercisability in the event of the Optionee’s death, disability or
retirement or, subject to Section 18.2 below, other events and may provide
for expiration prior to the end of its term in the event of the termination of
the Optionee’s service. Options may be awarded in combination with SARs, and
such an Award may provide that the Options will not be exercisable unless the
related SARs are forfeited.


 


5.5.         Effect
of Change in Control. The Committee may determine, at
the time of granting an Option or thereafter, that such Option shall become
exercisable as to all or part of the Common Shares subject to such Option in
the event that a Change in Control occurs with respect to the Company or in the
event that the Optionee is subject to an Involuntary Termination after a Change
in Control. In addition, acceleration of exercisability may be required under Section 12.3.


 


5.6.         Modification
or Assumption of Options. Within the limitations of
the Plan, the Committee may modify, extend or assume outstanding options or may
accept the cancellation of outstanding options (whether granted by the Company
or by another issuer) in return for the grant of new options for the same or a
different number of shares and at the same or a different exercise price,
except that the Company shall not effect a direct or indirect repricing of
outstanding options (including through an offer to exchange options or any buy
out or cash out of options) without stockholder approval. The foregoing
notwithstanding, no modification of an 


 


3

















 


Option shall, without the consent of the Optionee, alter or impair his
or her rights or obligations under such Option.


 


5.7.         Buyout
Provisions. The Committee may at any time (a) offer
to buy out for a payment in cash or cash equivalents an Option previously
granted or (b) authorize an Optionee to elect to cash out an Option
previously granted, in either case at such time and based upon such terms and
conditions as the Committee shall establish, provided, that, in each case of (a) and
(b), the Fair Market Value of a Common Share, at the time of such buy out or
cash out, is equal to or more than the Exercise Price of the Option.


 


ARTICLE 6.    PAYMENT FOR
OPTION SHARES.


 


6.1.         General
Rule. The entire Exercise Price of Common Shares
issued upon exercise of Options shall be payable in cash or cash equivalents at
the time when such Common Shares are purchased, except as follows:


 


(a)           In the case of an
ISO granted under the Plan, payment shall be made only pursuant to the express
provisions of the applicable Stock Option Agreement. The Stock Option Agreement
may specify that payment may be made in any form(s) described in this Article 6.


 


(b)           In the case of an
NSO, the Committee may at any time accept payment in any form(s) described
in this Article 6 in its sole discretion.


 


6.2.         Surrender
of Stock. To the extent permitted by the Committee,
all or any part of the Exercise Price may be paid by surrendering, or attesting
to the ownership of, Common Shares that are already owned by the Optionee. Such
Common Shares shall be valued at their Fair Market Value on the date when the
new Common Shares are purchased under the Plan.


 


6.3.         Exercise/Sale.
To the extent permitted by the Committee, all or any part of the Exercise Price
and any withholding taxes may be paid by delivering (on a form prescribed by
the Company) an irrevocable direction to a securities broker to sell all or
part of the Common Shares being purchased under the Plan and to deliver all or
part of the sales proceeds to the Company.


 


6.4.         Other
Forms of Payment. To the extent that this Section 6.4
is applicable, all or any part of the Exercise Price and any withholding taxes
may be paid in any other form that is consistent with applicable laws,
regulations and rules.


 


ARTICLE 7.    STOCK
APPRECIATION RIGHTS.


 


7.1.         SAR
Agreement. Each grant of a SAR under the Plan shall be
evidenced by a SAR Agreement between the Optionee and the Company. Such SAR
shall be subject to all applicable terms of the Plan and may be subject to any
other terms that are not inconsistent with the Plan. The provisions of the
various SAR Agreements entered into under the Plan need not be identical. SARs
may be granted in consideration of a reduction in the Optionee’s other
compensation.


 


4

















 


7.2.         Number
of Shares. Each SAR Agreement shall specify the number
of Common Shares to which the SAR pertains and shall provide for the adjustment
of such number in accordance with Article 12. SARs granted to any Optionee
in a single calendar year shall in no event pertain to more than 1,000,000
Common Shares. The limitations set forth in the preceding sentence shall be
subject to adjustment in accordance with Article 12.


 


7.3.         Exercise
Price. Each SAR Agreement shall specify the Exercise
Price. A SAR Agreement may specify an Exercise Price that varies in accordance
with a predetermined formula while the SAR is outstanding.


 


7.4.         Exercisability
and Term. Each SAR Agreement shall specify the date
when all or any installment of the SAR is to become exercisable. The SAR
Agreement shall also specify the term of the SAR. A SAR Agreement may provide
for accelerated exercisability in the event of the Optionee’s death, disability
or retirement or, subject to Section 18.2 below, other events and may
provide for expiration prior to the end of its term in the event of the
termination of the Optionee’s service. SARs may be awarded alone or in
combination with Options, and such an Award may provide that the SARs will not
be exercisable unless the related Options are forfeited. A SAR may be included
in an ISO only at the time of grant but may be included in an NSO at the time
of grant or thereafter.  A SAR granted
under the Plan may provide that it will be exercisable only in the event of a
Change in Control.


 


7.5.         Effect
of Change in Control. The Committee may determine, at
the time of granting a SAR or thereafter, that such SAR shall become fully
exercisable as to all Common Shares subject to such SAR in the event that the
Company is subject to a Change in Control or in the event that the Optionee is
subject to an Involuntary Termination after a Change in Control. In addition,
acceleration of exercisability may be required under Section 12.3.


 


7.6.         Exercise
of SARs. Upon exercise of a SAR, the Optionee (or any
person having the right to exercise the SAR after his or her death) shall
receive from the Company (a) Common Shares, (b) cash or (c) a
combination of Common Shares and cash, as the Committee shall determine. The
amount of cash and/or the Fair Market Value of Common Shares received upon
exercise of SARs shall, in the aggregate, be equal to the amount by which the
Fair Market Value (on the date of surrender) of the Common Shares underlying
the SARs exceeds the Exercise Price. If, on the date when a SAR expires, the
Exercise Price under such SAR is less than the Fair Market Value on such date
but any portion of such SAR has not been exercised or surrendered, then such
SAR shall automatically be deemed to be exercised as of such date with respect
to such portion.


 


7.7.         Modification
or Assumption of SARs.  Within the limitations of
the Plan, the Committee may modify, extend or assume outstanding SARs or may
accept the cancellation of outstanding SARs (whether granted by the Company or
by another issuer) in return for the grant of new SARs for the same or a
different number of shares and at the same or a different exercise price,
except that the Company shall not effect a direct or indirect repricing of
outstanding SARs (including through an offer to exchange SARs or any buy out or
cash out of SARs) without stockholder approval. The foregoing notwithstanding,
no modification of a SAR shall, without the consent of the Optionee, alter or
impair his or her rights or obligations under such SAR.


 


5

















 


ARTICLE 8.    RESTRICTED
SHARES.


 


8.1.         Restricted
Stock Agreement. Each grant of Restricted Shares under
the Plan shall be evidenced by a Restricted Stock Agreement between the
recipient and the Company. Such Restricted Shares shall be subject to all
applicable terms of the Plan and may be subject to any other terms that are not
inconsistent with the Plan. The provisions of the various Restricted Stock
Agreements entered into under the Plan need not be identical.


 


8.2.         Payment
for Awards. Subject to the following sentence,
Restricted Shares may be sold or awarded under the Plan for such consideration
as the Committee may determine, including (without limitation) cash, cash
equivalents, past services and future services. To the extent that an Award
consists of newly issued Restricted Shares, the consideration shall consist
exclusively of cash, cash equivalents or past services rendered to the Company
(or a Parent or Subsidiary) or, for the amount in excess of the par value of
such newly issued Restricted Shares, full-recourse promissory notes, as the
Committee may determine.


 


8.3.         Vesting
Conditions. Each Award of Restricted Shares may be
subject to vesting as determined by the Committee. Vesting shall occur, in full
or in installments, upon satisfaction of the conditions specified in the
Restricted Stock Agreement. For any Award of Restricted Shares which is to vest
solely on the basis of service or employment, a minimum period of three years
(which may include vesting in installments over such three-year period) shall
be required as condition to such vesting. A Restricted Stock Agreement may
provide for accelerated vesting in the event of the Participant’s death,
disability or retirement or, subject to Section 18.2 below, other events.
The Committee may determine, at the time of granting Restricted Shares or
thereafter, that all or part of such Restricted Shares shall become vested in
the event that a Change in Control occurs with respect to the Company or in the
event that the Participant is subject to an Involuntary Termination after a
Change in Control.


 


8.4.         Voting
and Dividend Rights. The holders of Restricted Shares
awarded under the Plan shall have the same voting, dividend and other rights as
the Company’s other stockholders. A Restricted Stock Agreement, however, may
require that the holders of Restricted Shares invest any cash dividends
received in additional Restricted Shares. Such additional Restricted Shares
shall be subject to the same conditions and restrictions as the Award with
respect to which the dividends were paid.


 


ARTICLE 9.    STOCK UNITS
AND RESTRICTED STOCK UNITS.


 


9.1.         Stock
Unit Agreement. Each grant of Stock Units under the
Plan shall be evidenced by a Stock Unit Agreement between the recipient and the
Company. Such Stock Units shall be subject to all applicable terms of the Plan
and may be subject to any other terms that are not inconsistent with the Plan.
The provisions of the various Stock Unit Agreements entered into under the Plan
need not be identical. Stock Units may be granted in consideration of a
reduction in the recipient’s other compensation.


 


9.2.         Payment
for Awards. To the extent that an Award is granted in
the form of Stock Units, no cash consideration shall be required of the Award
recipients.


 


6
















 


9.3.         Vesting Conditions.
Each Award of Stock Units may be subject to vesting as determined by the
Committee. Vesting shall occur, in full or in installments, upon satisfaction
of the conditions specified in the Stock Unit Agreement. For any Award of Stock
Units which is to vest solely on the basis of service or employment, a minimum
period of three years (which may include vesting in installments over such
three-year period) shall be required as condition to such vesting. A Stock Unit
Agreement may provide for accelerated vesting in the event of the Participant’s
death, disability or retirement or, subject to Section 18.2 below, other
events. The Committee may determine, at the time of granting Stock Units or
thereafter, that all or part of such Stock Units shall become vested in the
event that the Company is subject to a Change in Control or in the event that
the Participant is subject to an Involuntary Termination after a Change in
Control. In addition, acceleration of vesting may be required under Section 12.3.


 


9.4.         Voting and Dividend
Rights. The holders of Stock Units shall have no voting rights. Prior to
settlement or forfeiture, any Stock Unit awarded under the Plan may, at the
Committee’s discretion, carry with it a right to dividend equivalents. Such
right entitles the holder to be credited with an amount equal to all cash
dividends paid on one Common Share while the Stock Unit is outstanding.
Dividend equivalents may be converted into additional Stock Units. Settlement
of dividend equivalents may be made in the form of cash, in the form of Common
Shares, or in a combination of both. Prior to distribution, any dividend
equivalents which are not paid shall be subject to the same conditions and
restrictions as the Stock Units to which they attach.


 


9.5.         Form and Time of
Settlement of Stock Units. Settlement of vested Stock Units may be made in
the form of (a) cash, (b) Common Shares or (c) any combination
of both, as determined by the Committee. The actual number of Stock Units
eligible for settlement may be larger or smaller than the number included in
the original Award, based on predetermined performance factors. Methods of
converting Stock Units into cash may include (without limitation) a method
based on the average Fair Market Value of Common Shares over a series of
trading days. Vested Stock Units may be settled in a lump sum or in
installments. The distribution may occur or commence when all vesting
conditions applicable to the Stock Units have been satisfied or have lapsed, or
it may be deferred to any later date. The amount of a deferred distribution may
be increased by an interest factor or by dividend equivalents. Until an Award
of Stock Units is settled, the number of such Stock Units shall be subject to
adjustment pursuant to Article 12.


 


9.6.         Death of Recipient.
Any Stock Units Award that becomes payable after the recipient’s death shall be
distributed to the recipient’s beneficiary or beneficiaries. Each recipient of
a Stock Units Award under the Plan shall designate one or more beneficiaries
for this purpose by filing the prescribed form with the Company. A beneficiary
designation may be changed by filing the prescribed form with the Company at
any time before the Award recipient’s death. If no beneficiary was designated
or if no designated beneficiary survives the Award recipient, then any Stock
Units Award that becomes payable after the recipient’s death shall be
distributed to the recipient’s estate.


 


9.7.         Creditors’ Rights. A
holder of Stock Units shall have no rights other than those of a general
creditor of the Company. Stock Units represent an unfunded and unsecured 


 


7

















 


obligation of
the Company, subject to the terms and conditions of the applicable Stock Unit
Agreement.


 


ARTICLE
10.    OTHER EQUITY-BASED AWARDS.


 


Subject to limitations under applicable law, the Committee is
authorized to grant to participants such other awards that may be denominated
or payable in, valued in whole or in part by reference to, otherwise based on
or related to, the Common Shares or factors that may influence the value of the
Common Shares, (including without limitation convertible or exchangeable debt
securities, other rights convertible or exchangeable into Common Shares,
purchase rights for Common Shares, awards with value and payment contingent
upon the performance of the Company, a participating Affiliate or a business
unit of the Company or of a participating Affiliate or any other factors
designated by the Committee and awards valued by reference to the book value of
Common Shares or the value of securities of or the performance of any such
entity). The Committee shall determine the terms and conditions of such other
awards. Common Shares delivered pursuant to an award in the nature of a
purchase right granted under this Article 10 shall be purchased for such
consideration, paid for at such times, by such methods and in such forms
(including without limitation cash, Common Shares, other awards, notes or other
property) as the Committee shall determine. Cash awards, as an element of or
supplement to any other award under the Plan, may also be granted pursuant to
this Article 10.


 


ARTICLE
11.    PERFORMANCE-BASED AWARDS.


 


The Committee is authorized to grant performance awards denominated in
cash, Common Shares, other awards or a combination thereof, subject to the
following terms and conditions and to such other terms and conditions, not
inconsistent herewith, as the Committee shall determine:


 


11.1.       Performance Awards
Generally. Performance awards granted under the Plan may be earned upon
achievement or satisfaction of performance conditions specified by the
Committee. In addition, the Committee may specify that any other award shall
constitute a performance award by conditioning the right of a participant to
exercise the award or have it settled, and the timing thereof, upon achievement
or satisfaction of such performance conditions as may be specified by the
Committee. The Committee may use such business criteria and other measures of
performance as it may deem appropriate in establishing any performance
conditions, and may exercise its discretion to reduce or increase the amounts
payable under any award subject to performance conditions, except as limited
below in the case of a performance award intended to qualify as
performance-based compensation (within the meaning of section 162(m) of
the Internal Revenue Code of 1986, as amended (the “Code”)).


 


11.2.       Performance Awards Granted
to Covered Employees. If the Committee determines that a performance award
to be granted to an employee who is designated by the Committee as likely to be
a covered employee (within the meaning of section 162 (m) of
the Code) should qualify as performance-based compensation, the grant, exercise
and/or settlement of such performance award shall be contingent upon
achievement of a pre-established performance goal and other terms set forth in
this subsection. Common Shares awarded to any 


 


8

















 


Participant in
a single calendar year pursuant to this Article shall in no event pertain
to more than 500,000 shares. In the event of a cash-based performance award,
the value of an award granted to a Participant in any calendar year shall not
exceed $5,000,000.


 


(a)           Performance Goal.
The performance goal for performance awards shall consist of one or more
business criteria and a targeted level or levels of performance with respect to
each of such criteria, as specified by the Committee consistent with this
subsection. The performance goal shall be objective and shall otherwise meet
the requirements of section 162(m) of the Code (including the
requirement that the level or levels of performance targeted by the Committee
result in the achievement of performance goals being “substantially
uncertain”). The Committee may determine that such performance awards shall be
granted, exercised and/or settled upon achievement of any one performance goal
or that two or more of the performance goals must be achieved as a condition to
grant, exercise and/or settlement of such performance awards. Performance goals
may differ for performance awards granted to any one participant or to
different participants.


 


(b)           Business Criteria.
One or more of the following business criteria for the Company, on a
consolidated basis, and/or for an Affiliate or a business unit of the Company
or of an Affiliate shall be used by the Committee in establishing performance
goals for performance awards: (1) net sales or product and product related
revenue; (2) earnings from operations, earnings before or after taxes,
earnings before or after interest, depreciation, amortization or extraordinary
or special items, (3) net income or net income per Common Share (basic or
diluted); (4) return on assets, return on investment, return on capital,
or return on equity; (5) cash flow, free cash flow, cash flow return on
investment, or net cash provided by operations; (6) interest expense after
taxes; (7) economic value created; (8) operating margin; (9) share
price or total stockholder return; and (10) strategic business criteria
(including without limitation meeting specified market penetration, geographic
business expansion goals, cost targets, customer satisfaction, employee
satisfaction, management of employment practices and employee benefits, supervision
of information technology, and goals relating to acquisitions or divestitures
of specified Affiliates or business units of the Company or of Affiliates). The
targeted level or levels of performance with respect to such business criteria
may be established at such levels and in such terms as the Committee may
determine, in its discretion, including in absolute terms, as a goal relative
to performance in prior periods, or as a goal compared to the performance of
one or more comparable companies or an index covering multiple companies.


 


(c)           Performance Period;
Timing for Establishing Performance Goals. Achievement of performance goals
in respect of performance awards shall be measured over a performance period of
up to one year or more than one year, as specified by the Committee. A
performance goal shall be established not later than the earlier of (i) 90 days
after the beginning of any performance period applicable to such performance
award or (ii) the time when 25% of such performance period has elapsed.


 


9

















 


(d)           Settlement of
Performance Awards; Other Terms. Settlement of performance awards shall be
in cash, Common Shares, other awards or other property, in the discretion of
the Committee. The Committee may, in its discretion, increase or reduce the
amount of a settlement otherwise to be made in connection with performance
awards, but may not exercise discretion to increase any such amount payable to
a covered employee in respect of a performance award, subject to this
subsection. Any settlement which changes the form of payment from that
originally specified shall be implemented in a manner such that the performance
award and other related awards do not, solely for that reason, fail to qualify
as performance-based compensation. The Committee shall specify the
circumstances in which performance awards shall be paid or forfeited in the
event of termination of a participant’s employment by or directorship or
consultancy with the Company or an Affiliate or other event prior to the end of
a performance period or settlement of such performance awards.


 


11.3.       Written Determinations.
Determinations by the Committee as to the establishment of performance goals,
the amount potentially payable in respect of performance awards and annual
incentive awards, the level of actual achievement of the specified performance
goals relating to performance awards and annual incentive awards and the amount
of any final performance award and annual incentive award shall be recorded in
writing in the case of performance awards intended to qualify under
section 162(m) of the Code. Specifically, the Committee shall certify
in writing, in a manner conforming to applicable regulations under
section 162(m) of the Code, prior to settlement of each such award
granted to a covered employee, that the performance objective relating to the
performance award and other material terms of the award upon which settlement
of the award was conditioned have been satisfied.


 


ARTICLE
12.    PROTECTION AGAINST DILUTION.


 


12.1.       Adjustments. In the
event of a subdivision of the outstanding Common Shares, a declaration of a
dividend payable in Common Shares or a combination or consolidation of the
outstanding Common Shares (by reclassification or otherwise) into a lesser
number of Common Shares, corresponding adjustments shall automatically be made
in each of the following:


 


(a)           The
number of Options, SARs, Restricted Shares and Stock Units available for future
Awards under Article 3;


 


(b)           The
limitations set forth in Sections 5.2 and 7.2;


 


(c)           The
number of Common Shares covered by each outstanding Option and SAR;


 


(d)           The
Exercise Price under each outstanding Option and SAR; or


 


(e)           The
number of Stock Units included in any prior Award which has not yet been
settled.


 


10

















 


In the event of a declaration of an extraordinary dividend payable in a
form other than Common Shares in an amount that has a material effect on the
price of Common Shares, a recapitalization, a spin-off or a similar occurrence,
the Committee shall make such adjustments as it, in its sole discretion, deems
appropriate in one or more of the foregoing. Except as provided in this Article 12,
a Participant shall have no rights by reason of any issuance by the Company of
stock of any class or securities convertible into stock of any class, any
subdivision or consolidation of shares of stock of any class, the payment of
any stock dividend or any other increase or decrease in the number of shares of
stock of any class.


 


12.2.       Dissolution or Liquidation.
To the extent not previously exercised or settled, Options, SARs and Stock
Units shall terminate immediately prior to the dissolution or liquidation of
the Company.


 


12.3.       Reorganizations. In the
event that the Company is a party to a merger or other reorganization,
outstanding Awards shall be subject to the agreement of merger or
reorganization. Such agreement shall provide for (a) the continuation of
the outstanding Awards by the Company, if the Company is a surviving
corporation, (b) the assumption of the outstanding Awards by the surviving
corporation or its parent or subsidiary, (c) the substitution by the
surviving corporation or its parent or subsidiary of its own awards for the
outstanding Awards, (d) full exercisability or vesting and accelerated
expiration of the outstanding Awards or (e) settlement of the full value
of the outstanding Awards in cash or cash equivalents followed by cancellation
of such Awards.


 


ARTICLE
13.    DEFERRAL OF AWARDS.


 


The Committee (in its sole discretion) may permit or require a
Participant to:


 


(a)           Have
cash that otherwise would be paid to such Participant as a result of the
exercise of a SAR or the settlement of Stock Units credited to a deferred
compensation account established for such Participant by the Committee as an
entry on the Company’s books;


 


(b)           Have
Common Shares that otherwise would be delivered to such Participant as a result
of the exercise of an Option or SAR converted into an equal number of Stock
Units; or


 


(c)           Have
Common Shares that otherwise would be delivered to such Participant as a result
of the exercise of an Option or SAR or the settlement of Stock Units converted
into amounts credited to a deferred compensation account established for such
Participant by the Committee as an entry on the Company’s books. Such amounts
shall be determined by reference to the Fair Market Value of such Common Shares
as of the date when they otherwise would have been delivered to such
Participant.


 


A deferred
compensation account established under this Article 13 may be credited
with interest or other forms of investment return, as determined by the
Committee. A Participant for whom such an account is established shall have no
rights other than those of a general creditor of the 


 


11

















 


Company. Such
an account shall represent an unfunded and unsecured obligation of the Company
and shall be subject to the terms and conditions of the applicable agreement
between such Participant and the Company. If the deferral or conversion of
Awards is permitted or required, the Committee (in its sole discretion) may
establish rules, procedures and forms pertaining to such Awards, including
(without limitation) the settlement of deferred compensation accounts
established under this Article 13.


 


ARTICLE 14.    AWARDS
UNDER OTHER PLANS.


 


The Company may grant awards under other plans or programs. Such awards
may be settled in the form of Common Shares issued under this Plan. Such Common
Shares shall be treated for all purposes under the Plan like Common Shares
issued in settlement of Stock Units and shall, when issued, reduce the number
of Common Shares available under Article 3.


 


ARTICLE 15.    PAYMENT OF
DIRECTOR’S FEES IN SECURITIES.


 


15.1.       Effective Date. No
provision of this Article 15 shall be effective unless and until the Board
has determined to implement such provision.


 


15.2.       Elections to Receive NSOs,
Restricted Shares or Stock Units. An Outside Director may elect to receive
his or her annual retainer payments and/or meeting fees from the Company in the
form of cash, NSOs, Restricted Shares or Stock Units, or a combination thereof,
as determined by the Board. Such NSOs, Restricted Shares and Stock Units shall
be issued under the Plan.


 


15.3.       Number and Terms of NSOs,
Restricted Shares or Stock Units. The number of NSOs, Restricted Shares or
Stock Units to be granted to Outside Directors in lieu of annual retainers and
meeting fees that would otherwise be paid in cash shall be calculated in a manner
determined by the Board. The terms of such NSOs, Restricted Shares or Stock
Units shall also be determined by the Board.


 


ARTICLE 16.    LIMITATION
ON RIGHTS.


 


16.1.       Retention Rights.
Neither the Plan nor any Award granted under the Plan shall be deemed to give
any individual a right to remain an Employee, Outside Director or Consultant.
The Company and its Parents, Subsidiaries and Affiliates reserve the right to
terminate the service of any Employee, Outside Director or Consultant at any
time.


 


16.2.       Stockholders’ Rights. A
Participant shall have no dividend rights, voting rights or other rights as a
stockholder with respect to any Common Shares covered by his or her Award prior
to the time when a stock certificate for such Common Shares is issued or, if
applicable, the time when he or she becomes entitled to receive such Common
Shares by filing any required notice of exercise and paying any required
Exercise Price. No adjustment shall be made for cash dividends or other rights
for which the record date is prior to such time, except as expressly provided
in the Plan.


 


12

















 


16.3.       Regulatory Requirements.
Any other provision of the Plan notwithstanding, the obligation of the Company
to issue Common Shares under the Plan shall be subject to all applicable laws, rules and
regulations and such approval by any regulatory body as may be required. The
Company reserves the right to restrict, in whole or in part, the delivery of
Common Shares pursuant to any Award prior to the satisfaction of all legal
requirements relating to the issuance of such Common Shares, to their
registration, qualification or listing or to an exemption from registration,
qualification or listing.


 


ARTICLE
17.    WITHHOLDING TAXES.


 


17.1.       General. A Participant
or his or her successor shall make arrangements satisfactory to the Company for
the satisfaction of any obligations of the Company to withhold income and
employment taxes under applicable federal, state, local or foreign law in
connection with Awards under the Plan. The Company shall not be required to
issue any Common Shares or make any cash payment under the Plan until such
obligations are satisfied.


 


17.2.       Withholding in Shares.
The Committee may permit such Participant to satisfy all or part of such tax
withholding obligations by having the Company withhold all or a portion of any
Common Shares that otherwise would be issued to him or her or by surrendering
all or a portion of any Common Shares that he or she previously acquired. Such Common
Shares shall be valued at their Fair Market Value on the date when they are
withheld or surrendered.


 


ARTICLE 18.    FUTURE OF
THE PLAN.


 


18.1.       Term of the Plan. The
Plan, as set forth herein, became effective on March 9, 2000. Unless
earlier terminated pursuant to Section 18.2, the Plan shall remain in
effect until February 6, 2018.


 


18.2.       Amendment or Termination.
The Board may, at any time and for any reason, amend or terminate the Plan. An
amendment of the Plan shall be subject to the approval of the Company’s
stockholders only to the extent required by applicable laws, regulations or
rules. No Awards shall be granted under the Plan after the termination thereof.
The termination of the Plan, or any amendment thereof, shall not affect any
Award previously granted under the Plan. Notwithstanding anything to the
contrary herein, from and after June 11, 2008, the vesting schedule (or
the time at which any restriction may lapse) with respect to any Awards may not
be accelerated except in the cases of death, disability or retirement of the
participant or in connection with a Change in Control of the Company; provided that Awards for no more than 10% of the total
number of shares authorized under the Plan may be accelerated upon other
events.


 


18.3        No Repricings.  Except in connection with a corporate
transaction involving the Company (including, without limitation, any stock
dividend, stock split, extraordinary cash dividend, recapitalization,
reorganization, merger, consolidation, split-up, spin-off, combination, or
exchange of shares), the terms of outstanding awards may not be amended to
reduce the exercise price of outstanding Options or SARs or cancel outstanding
Options or SARs in 


 


13

















 


exchange for cash, other awards
or Options or SARs with an exercise price that is less than the exercise price
of the original Options or SARs without stockholder approval.


 


ARTICLE
19.    DEFINITIONS.


 


19.1.       “Affiliate” means any
entity other than a Subsidiary, if the Company and/or one or more Subsidiaries
own not less than 50% of such entity.


 


19.2.       “Award” means any award
of an Option, a SAR, a Restricted Share or a Stock Unit under the Plan.


 


19.3.       “Board” means the
Company’s Board of Directors, as constituted from time to time.


 


19.4.       “Cause” shall mean (a) the
unauthorized use or disclosure of the confidential information or trade secrets
of the Company, which use or disclosure causes material harm to the Company, (b) conviction
of, or a plea of “guilty” or “no contest” to, a felony under the laws of the
United States or any State thereof, (c) gross negligence, (d) willful
misconduct or (e) a failure to perform assigned duties that continues
after the Participant has received written notice of such failure from the
Board. The foregoing, however, shall not be deemed an exclusive list of all
acts or omissions that the Company (or the Parent, Subsidiary or Affiliate
employing the Participant) may consider as grounds for the discharge of the
Participant without Cause.


 


19.5.       “Change in Control”
shall mean:


 


(a)           The
consummation of a merger or consolidation of the Company with or into another
entity or any other corporate reorganization, if persons who were not
stockholders of the Company immediately prior to such merger, consolidation or
other reorganization own immediately after such merger, consolidation or other
reorganization 50% or more of the voting power of the outstanding securities of
each of (i) the continuing or surviving entity and (ii) any direct or
indirect parent corporation of such continuing or surviving entity;


 


(b)           The
sale, transfer or other disposition of all or substantially all of the
Company’s assets;


 


(c)           A
change in the composition of the Board, as a result of which fewer than 80% of
the incumbent directors are directors who either (i) had been directors of
the Company on the date 24 months prior to the date of the event that may
constitute a Change in Control (the “original directors”) or (ii) were
elected, or nominated for election, to the Board with the affirmative votes of
at least a majority of the aggregate of the original directors who were still
in office at the time of the election or nomination and the directors whose
election or nomination was previously so approved; or


 


(d)           Any
transaction as a result of which any person is the “beneficial owner” (as
defined in Rule 13d-3 under the Exchange Act), directly or indirectly, of
securities of 


 


14

















 


the Company representing at least 50% of the total voting power
represented by the Company’s then outstanding voting securities. For purposes
of this Paragraph (d), the term “person” shall have the same meaning as
when used in sections 13(d) and 14(d) of the Exchange Act but shall
exclude (i) a trustee or other fiduciary holding securities under an
employee benefit plan of the Company or of a Parent or Subsidiary and (ii) a
corporation owned directly or indirectly by the stockholders of the Company in
substantially the same proportions as their ownership of the common stock of
the Company.


 


A transaction
shall not constitute a Change in Control if its sole purpose is to change the
state of the Company’s incorporation or to create a holding company that will
be owned in substantially the same proportions by the persons who held the
Company’s securities immediately before such transaction.


 


19.6.       “Code” means the
Internal Revenue Code of 1986, as amended.


 


19.7.       “Committee” means a
committee of the Board, as described in Article 2.


 


19.8.       “Common Share” means
one share of the common stock of the Company.


 


19.9.       “Company” means
Affymetrix, Inc., a Delaware corporation.


 


19.10.     “Consultant” means a
consultant or adviser who provides bona fide services to the Company, a Parent,
a Subsidiary or an Affiliate as an independent contractor. Service as a
Consultant shall be considered employment for all purposes of the Plan, except
as provided in Section 4.1.


 


19.11.     “Employee” means a
common-law employee of the Company, a Parent, a Subsidiary or an Affiliate.


 


19.12.     “Exchange Act” means the
Securities Exchange Act of 1934, as amended.


 


19.13.     “Exercise Price,” in the
case of an Option, means the amount for which one Common Share may be purchased
upon exercise of such Option, as specified in the applicable Stock Option
Agreement. “Exercise Price,” in the case of a SAR, means an amount, as
specified in the applicable SAR Agreement, which is subtracted from the Fair
Market Value of one Common Share in determining the amount payable upon
exercise of such SAR.


 


19.14.     “Fair Market Value” means
the market price of Common Shares, determined by the Committee in good faith on
such basis as it deems appropriate. Whenever possible, the determination of
Fair Market Value by the Committee shall be based on the prices reported in The Wall Street Journal. Such
determination shall be conclusive and binding on all persons.


 


19.15.     “Involuntary Termination”
means the termination of the Participant’s service by reason of:


 


15

















 


(a)           The
involuntary discharge of the Participant by the Company (or the Parent,
Subsidiary or Affiliate employing him or her) for reasons other than Cause; or


 


(b)           The
voluntary resignation of the Participant following (i) a material adverse
change in his or her title, stature, authority or responsibilities with the
Company (or the Parent, Subsidiary or Affiliate employing him or her), (ii) a
material reduction in his or her base salary or (iii) receipt of notice
that his or her principal workplace will be relocated by more than 30 miles.


 


19.16.     “ISO” means an incentive
stock option described in section 422(b) of the Code.


 


19.17.     “NSO” means a stock
option not described in sections 422 or 423 of the Code.


 


19.18.     “Option” means an ISO or
NSO granted under the Plan and entitling the holder to purchase Common Shares.


 


19.19.     “Optionee” means an
individual or estate who holds an Option or SAR.


 


19.20.     “Outside Director” shall
mean a member of the Board who is not an Employee. Service as an Outside
Director shall be considered employment for all purposes of the Plan, except as
provided in Section 4.1.


 


19.21.     “Parent” means any
corporation (other than the Company) in an unbroken chain of corporations
ending with the Company, if each of the corporations other than the Company
owns stock possessing 50% or more of the total combined voting power of all
classes of stock in one of the other corporations in such chain. A corporation
that attains the status of a Parent on a date after the adoption of the Plan
shall be considered a Parent commencing as of such date.


 


19.22.     “Participant” means an
individual or estate who holds an Award.


 


19.23.     “Plan” means this
Affymetrix, Inc. 2000 Equity Incentive Plan, as amended from time to time.


 


19.24.     “Restricted Share” means
a Common Share awarded under Article 8 of the Plan.


 


19.25.     “Restricted Stock Agreement”
means the agreement between the Company and the recipient of a Restricted Share
which contains the terms, conditions and restrictions pertaining to such
Restricted Share.


 


19.26.     “SAR” means a stock
appreciation right granted under the Plan.


 


19.27.     “SAR Agreement” means the
agreement between the Company and an Optionee which contains the terms,
conditions and restrictions pertaining to his or her SAR.


 


19.28.     “Stock Option Agreement”
means the agreement between the Company and an Optionee that contains the
terms, conditions and restrictions pertaining to his or her Option.


 


16

















 


19.29.     “Stock Unit” means a
bookkeeping entry representing the equivalent of one Common Share or the right
to receive a specified number of Common Shares (including restricted stock
units), as awarded under the Plan.


 


19.30.     “Stock Unit Agreement”
means the agreement between the Company and the recipient of a Stock Unit which
contains the terms, conditions and restrictions pertaining to such Stock Unit.


 


19.31.     “Subsidiary” means any
corporation (other than the Company) in an unbroken chain of corporations
beginning with the Company, if each of the corporations other than the last
corporation in the unbroken chain owns stock possessing 50% or more of the
total combined voting power of all classes of stock in one of the other
corporations in such chain. A corporation that attains the status of a
Subsidiary on a date after the adoption of the Plan shall be considered a
Subsidiary commencing as of such date.


 


ARTICLE
20.    EXECUTION.


 


To record the amendment and restatement of the Plan by the Board on February 6,
2008, the amendment and restatement of the Plan by the Compensation Committee
of the Board on April 2, 2008, May 29, 2008 and June 23, 2008
and the approval of such amendment and restatement by the stockholders of the
Company on June 11, 2008, the Company has caused its duly authorized
officer to execute this document in the name of the Company.


 


	
   

  	
  AFFYMETRIX,
  INC.

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
  By 

  	
  /s/ Stephen
  P.A. Fodor, Ph.D.

  
	
   

  	
  Name:
  Stephen P.A. Fodor, Ph.D.

  
	
   

  	
  Title: Chairman and Chief Executive Officer

  



 


17